A two-dimension convection-dispersion-biodynamics model was given to simulate the treatment efficiency of two-stage subsurface vertical flow constructed wetlands for urban stormwater runoff of Chongqing. Focus on the following 4 types of boundary conditions: Atmospheric Boundary-Seepage Face, Atmospheric Boundary-incomplete Seepage Face 1 (uniformlyspaced effluent), Atmospheric Boundary- incomplete Seepage Face 2 (A-S2’s space is 2 times larger than A-S1‘s), Atmospheric Boundary-Constant Head. The simulated results show that under the same working condition, the A-S2 boundary condition has an obviously better performance on the transportation of dissolved oxygen and the treatment efficiency of COD,nitrogen and phosphorus removal , since the specific effluent mode offers a better hydraulic characteristic of the constructed wetland.